All 3 early Evo's have this EGR port in the head, even though only the III has the EGR fitting on the inlet manifold, and receptacle on the pipe leading to the throttlebody.
As far as I've been led to believe, the reasoning for all 3 having this port in the head, along with the stock ECU's having the coding and tables for it (albeit disabled) is it was used in the WRC cars anti-lag systems.
When they developed the III, they incorporated this port into a dedicated EGR system.
I might be wrong, but it sounds feasible.
Otherwise, all 3 manifolds are interchangeable, and with the exception of an additional vacuum port on the III's manifold, they are identical. The I and II manifolds will cover that port happily enough though.
The biggest laugh of it all, is the EGR system has never worked from the factory. I've never seen any III with a functioning banjo bolt screwed into the head. Every bolt has been a solid one, with no actual flow path through it. Weird...